update session_to_nwb

src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_convert_session.py

@@ -1,69 +1,108 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
+import os
 from pathlib import Path
 from typing import Union
-import datetime
-from zoneinfo import ZoneInfo
 
+from dateutil import tz
+from neuroconv.datainterfaces import OpenEphysBinaryRecordingInterface
 from neuroconv.utils import load_dict_from_file, dict_deep_update
 
 from constantinople_lab_to_nwb.schierek_embargo_2024 import SchierekEmbargo2024NWBConverter
 
 
-def session_to_nwb(data_dir_path: Union[str, Path], output_dir_path: Union[str, Path], stub_test: bool = False):
-
-    data_dir_path = Path(data_dir_path)
-    output_dir_path = Path(output_dir_path)
-    if stub_test:
-        output_dir_path = output_dir_path / "nwb_stub"
-    output_dir_path.mkdir(parents=True, exist_ok=True)
-
-    session_id = "subject_identifier_usually"
-    nwbfile_path = output_dir_path / f"{session_id}.nwb"
-
+def session_to_nwb(
+        openephys_recording_folder_path: Union[str, Path],
+        nwbfile_path: Union[str, Path],
+        stub_test: bool = False,
+        overwrite: bool = False,
+):
+    """
+    Convert a session of data to NWB format.
+
+    Parameters
+    ----------
+    openephys_recording_folder_path : str or Path
+        The path to the OpenEphys recording folder.
+    nwbfile_path : str or Path
+        The path to the NWB file to write.
+    stub_test : bool, default: False
+        Whether to run a stub test conversion.
+    overwrite : bool, default: False
+        Whether to overwrite an existing NWB file.
+    """
     source_data = dict()
     conversion_options = dict()
 
     # Add Recording
-    source_data.update(dict(Recording=dict()))
-    conversion_options.update(dict(Recording=dict(stub_test=stub_test)))
+    stream_names = OpenEphysBinaryRecordingInterface.get_stream_names(folder_path=openephys_recording_folder_path)
+    stream_name_raw = [stream_name for stream_name in stream_names if "AP" in stream_name][0]
+    stream_name_lfp = [stream_name for stream_name in stream_names if "LFP" in stream_name][0]
+
+    source_data.update(
+        dict(
+            RecordingAP=dict(folder_path=openephys_recording_folder_path, stream_name=stream_name_raw),
+            RecordingLFP=dict(folder_path=openephys_recording_folder_path, stream_name=stream_name_lfp),
+        ),
+    )
+    conversion_options.update(
+        dict(
+            RecordingAP=dict(stub_test=stub_test),
+            RecordingLFP=dict(stub_test=stub_test, write_as="lfp"),
+        ),
+    )
 
     # Add Sorting
-    source_data.update(dict(Sorting=dict()))
-    conversion_options.update(dict(Sorting=dict()))
+    # source_data.update(dict(Sorting=dict()))
+    # conversion_options.update(dict(Sorting=dict()))
 
     # Add Behavior
-    source_data.update(dict(Behavior=dict()))
-    conversion_options.update(dict(Behavior=dict()))
+    # source_data.update(dict(Behavior=dict()))
+    # conversion_options.update(dict(Behavior=dict()))
+
+    recording_folder_name = Path(openephys_recording_folder_path).parent.stem
+    subject_id, session_id = recording_folder_name.split("_", maxsplit=1)
 
     converter = SchierekEmbargo2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
     metadata = converter.get_metadata()
-    datetime.datetime(
-        year=2020, month=1, day=1, tzinfo=ZoneInfo("US/Eastern")
+    session_start_time = metadata["NWBFile"]["session_start_time"]
+    tzinfo = tz.gettz("America/New_York")
+    metadata["NWBFile"].update(
+        session_start_time=session_start_time.replace(tzinfo=tzinfo),
+        session_id=session_id,
     )
-    date = datetime.datetime.today()  # TO-DO: Get this from author
-    metadata["NWBFile"]["session_start_time"] = date
 
     # Update default metadata with the editable in the corresponding yaml file
     editable_metadata_path = Path(__file__).parent / "schierek_embargo_2024_metadata.yaml"
     editable_metadata = load_dict_from_file(editable_metadata_path)
     metadata = dict_deep_update(metadata, editable_metadata)
 
-    metadata["Subject"]["subject_id"] = "a_subject_id"  # Modify here or in the yaml file
+    metadata["Subject"].update(subject_id=subject_id)
 
     # Run conversion
-    converter.run_conversion(metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options)
+    converter.run_conversion(
+        nwbfile_path=nwbfile_path,
+        metadata=metadata,
+        conversion_options=conversion_options,
+        overwrite=overwrite,
+    )
 
 
 if __name__ == "__main__":
 
     # Parameters for conversion
-    data_dir_path = Path("/Directory/With/Raw/Formats/")
-    output_dir_path = Path("~/conversion_nwb/")
-    stub_test = False
-
-    session_to_nwb(data_dir_path=data_dir_path,
-                    output_dir_path=output_dir_path,
-                    stub_test=stub_test,
-                    )
+    recording_folder_path = Path("/Volumes/t7-ssd/GCP/Constantinople/J076_2023-12-06_13-24-28/Record Node 117")
+    nwbfile_path = Path("/Volumes/t7-ssd/GCP/Constantinople/nwbfiles/J076_2023-12-06_13-24-28.nwb")
+    if not nwbfile_path.parent.exists():
+        os.makedirs(nwbfile_path.parent, exist_ok=True)
+
+    stub_test = True
+    overwrite = True
+
+    session_to_nwb(
+        openephys_recording_folder_path=recording_folder_path,
+        nwbfile_path=nwbfile_path,
+        stub_test=stub_test,
+        overwrite=overwrite,
+    )